You might want to try looking at the fugue utility in FSL (http://www.fmrib.ox.ac.uk/fsl/fugue/index.html). I've read on the mailing list of ways that you can substitute a magnitude image.

Best,
Michael

On Mon, Jun 1, 2009 at 10:02 AM, Winston Chiong <[log in to unmask]> wrote:
Dear list users,

We've been testing subjects on a task on which we're expecting a lot of orbitofrontal and anterior temporal activation, and I had been anticipating using the FieldMap utility to correct for susceptibility artifact. Unfortunately, I've just learned that the GRE field mapping sequence that we've been acquiring has been saving the phase data only, without the magnitude data. (We're using a Siemens 3T TIM Trio scanner, acquiring a GRE field map with TEs of 5.19 and 7.65ms, echo spacing of 0.8 and 118 echoes.) Whereas, it looks like the FieldMap toolbox expects to have one phase and one magnitude image.

According to our Siemens rep, there's no way to reconstruct the magnitude data from the phase volume that we have; however, he seemed to think that the unwarping should be possible with the phase images only. Does anyone on the list know of tools that can be used to do this in place of FieldMap, or of a way to use the data that I've got to generate the data that FieldMap expects? (Browsing through the list archives, it looks like SPM wants the magnitude data in order to assess the SNR at each voxel--can I use any of my other structural or functional images to generate this?)


Thanks,
Winston




--
Research Associate
Gazzaley Lab
Department of Neurology
University of California, San Francisco